<?xml version="1.0" encoding="ascii"?>
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
          "DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
<head>
  <title>moltk.Biosequence</title>
  <link rel="stylesheet" href="epydoc.css" type="text/css" />
  <script type="text/javascript" src="epydoc.js"></script>
</head>

<body bgcolor="white" text="black" link="blue" vlink="#204080"
      alink="#204080">
<!-- ==================== NAVIGATION BAR ==================== -->
<table class="navbar" border="0" width="100%" cellpadding="0"
       bgcolor="#a0c0ff" cellspacing="0">
  <tr valign="middle">
  <!-- Home link -->
      <th>&nbsp;&nbsp;&nbsp;<a
        href="moltk-module.html">Home</a>&nbsp;&nbsp;&nbsp;</th>

  <!-- Tree link -->
      <th>&nbsp;&nbsp;&nbsp;<a
        href="module-tree.html">Trees</a>&nbsp;&nbsp;&nbsp;</th>

  <!-- Index link -->
      <th>&nbsp;&nbsp;&nbsp;<a
        href="identifier-index.html">Indices</a>&nbsp;&nbsp;&nbsp;</th>

  <!-- Help link -->
      <th>&nbsp;&nbsp;&nbsp;<a
        href="help.html">Help</a>&nbsp;&nbsp;&nbsp;</th>

  <!-- Project homepage -->
      <th class="navbar" align="right" width="100%">
        <table border="0" cellpadding="0" cellspacing="0">
          <tr><th class="navbar" align="center"
            ><a class="navbar" target="_top" href="http://moltk.rotatingpenguin.com/">MolTK python API v0.4.0 Documentation</a></th>
          </tr></table></th>
  </tr>
</table>
<table width="100%" cellpadding="0" cellspacing="0">
  <tr valign="top">
    <td width="100%">
      <span class="breadcrumbs">
        <a href="moltk-module.html">Package&nbsp;moltk</a> ::
        Class&nbsp;Biosequence
      </span>
    </td>
    <td>
      <table cellpadding="0" cellspacing="0">
        <!-- hide/show private -->
        <tr><td align="right"><span class="options">[<a href="javascript:void(0);" class="privatelink"
    onclick="toggle_private();">hide&nbsp;private</a>]</span></td></tr>
        <tr><td align="right"><span class="options"
            >[<a href="frames.html" target="_top">frames</a
            >]&nbsp;|&nbsp;<a href="moltk.Biosequence-class.html"
            target="_top">no&nbsp;frames</a>]</span></td></tr>
      </table>
    </td>
  </tr>
</table>
<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class Biosequence</h1><p class="nomargin-top"></p>
<center>
<center>  <map id="uml_class_diagram_for_moltk_bi" name="uml_class_diagram_for_moltk_bi">
<area shape="rect" id="node1_17" href="moltk.Biosequence-class.html#__instance_size__" title="moltk.Biosequence.__instance_size__" alt="" coords="17,199,185,217"/>
<area shape="rect" id="node1_18" href="moltk.Biosequence-class.html#__init__" title="__init__( (object)arg1) &#45;&gt; None :" alt="" coords="17,220,185,239"/>
<area shape="rect" id="node1_19" href="moltk.Biosequence-class.html#__repr__" title="__repr__( (Biosequence)arg1) &#45;&gt; str : &#160;&#160;&#160;&#160;string representation" alt="" coords="17,239,185,257"/>
<area shape="rect" id="node1_20" href="moltk.Biosequence-class.html#__str__" title="__str__( (Biosequence)arg1) &#45;&gt; object :" alt="" coords="17,257,185,276"/>
<area shape="rect" id="node1_21" href="moltk.Biosequence-class.html#fasta" title="fasta( (Biosequence)arg1) &#45;&gt; str : &#160;&#160;&#160;&#160;&#160;Create a string representing the sequence in fasta format." alt="" coords="17,276,185,295"/>
<area shape="rect" id="node1_22" href="moltk.Biosequence-class.html#get_description" title="get_description( (Biosequence)arg1) &#45;&gt; str :" alt="" coords="17,295,185,313"/>
<area shape="rect" id="node1_23" href="moltk.Biosequence-class.html#get_number_of_residues" title="get_number_of_residues( (Biosequence)arg1) &#45;&gt; int :" alt="" coords="17,313,185,332"/>
<area shape="rect" id="node1_24" href="moltk.Biosequence-class.html#get_residue" title="get_residue( (Biosequence)arg1, (int)ix) &#45;&gt; BiosequenceResidue :" alt="" coords="17,332,185,351"/>
<area shape="rect" id="node1_25" href="moltk.Biosequence-class.html#load_fasta" title="load_fasta( (Biosequence)arg1, (str)file_name) &#45;&gt; Biosequence :" alt="" coords="17,351,185,369"/>
<area shape="rect" id="node1_26" href="moltk.Biosequence-class.html#load_stream" title="load_stream( (Biosequence)arg1, (object)is) &#45;&gt; None :" alt="" coords="17,369,185,388"/>
<area shape="rect" id="node1_27" href="moltk.Biosequence-class.html#repr" title="repr( (Biosequence)arg1) &#45;&gt; str : &#160;&#160;&#160;&#160;&#160;repr is a helper for the python __repr__ method." alt="" coords="17,388,185,407"/>
<area shape="rect" id="node1_28" href="moltk.Biosequence-class.html#write_fasta" title="write_fasta( (Biosequence)arg1, (object)os) &#45;&gt; None : &#160;&#160;&#160;&#160;&#160;Write sequence in fasta format to a C++ stream." alt="" coords="17,407,185,425"/>
<area shape="rect" id="node1_29" href="moltk.Biosequence-class.html#write_sequence_string" title="write_sequence_string( (Biosequence)arg1, (object)os) &#45;&gt; None : &#160;&#160;&#160;&#160;&#160;Write a sequence string to a C++ stream." alt="" coords="17,425,185,444"/>
<area shape="rect" id="node1_30" href="moltk.Biosequence-class.html#write_to_stream" title="write_to_stream( (Biosequence)arg1, (object)os) &#45;&gt; None :" alt="" coords="17,444,185,463"/>
<area shape="rect" id="node1" href="moltk.Biosequence-class.html" title="A macromolecule sequence (DNA or RNA or protein)" alt="" coords="5,174,197,469"/>
<area shape="rect" id="node2_31" href="moltk.BaseBiosequence.BaseResidue-class.html" title="Parent class for macromolecule sequence residues (nucleotides or amino &#160;acids)" alt="" coords="48,108,155,127"/>
<area shape="rect" id="node2_32" href="moltk.BaseBiosequence-class.html#__reduce__" title="helper for pickle" alt="" coords="48,129,155,148"/>
<area shape="rect" id="node2" href="moltk.BaseBiosequence-class.html" title="Parent class for macromolecule sequences and structures." alt="" coords="36,83,167,154"/>
<area shape="rect" id="node3_33" href="javascript:void(0);" title="??.instance.__new__" alt="" coords="43,39,159,57"/>
<area shape="rect" id="node3" href="javascript:void(0);" title="??.instance" alt="" coords="30,6,170,63"/>
</map>
  <img src="uml_class_diagram_for_moltk_bi.gif" alt='' usemap="#uml_class_diagram_for_moltk_bi" ismap="ismap" class="graph-without-title" />
</center>
</center>
<hr />
<p>A macromolecule sequence (DNA or RNA or protein)</p>

<!-- ==================== NESTED CLASSES ==================== -->
<a name="section-NestedClasses"></a>
<table class="summary" border="1" cellpadding="3"
       cellspacing="0" width="100%" bgcolor="white">
<tr bgcolor="#70b0f0" class="table-header">
  <td colspan="2" class="table-header">
    <table border="0" cellpadding="0" cellspacing="0" width="100%">
      <tr valign="top">
        <td align="left"><span class="table-header">Nested Classes</span></td>
        <td align="right" valign="top"
         ><span class="options">[<a href="#section-NestedClasses"
         class="privatelink" onclick="toggle_private();"
         >hide private</a>]</span></td>
      </tr>
    </table>
  </td>
</tr>
  <tr>
    <td colspan="2" class="summary">
    <p class="indent-wrapped-lines"><b>Inherited from <code><a href="moltk.BaseBiosequence-class.html">BaseBiosequence</a></code></b>:
      <code><a href="moltk.BaseBiosequence.BaseResidue-class.html">BaseResidue</a></code>
      </p>
    </td>
  </tr>
</table>
<!-- ==================== INSTANCE METHODS ==================== -->
<a name="section-InstanceMethods"></a>
<table class="summary" border="1" cellpadding="3"
       cellspacing="0" width="100%" bgcolor="white">
<tr bgcolor="#70b0f0" class="table-header">
  <td colspan="2" class="table-header">
    <table border="0" cellpadding="0" cellspacing="0" width="100%">
      <tr valign="top">
        <td align="left"><span class="table-header">Instance Methods</span></td>
        <td align="right" valign="top"
         ><span class="options">[<a href="#section-InstanceMethods"
         class="privatelink" onclick="toggle_private();"
         >hide private</a>]</span></td>
      </tr>
    </table>
  </td>
</tr>
<tr>
    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
      <table width="100%" cellpadding="0" cellspacing="0" border="0">
        <tr>
          <td><span class="summary-sig"><a href="moltk.Biosequence-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">...</span>)</span><br />
      __init__( (object)arg1) -&gt; None :</td>
          <td align="right" valign="top">
            
            
          </td>
        </tr>
      </table>
      
    </td>
  </tr>
<tr>
    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
      <table width="100%" cellpadding="0" cellspacing="0" border="0">
        <tr>
          <td><span class="summary-sig"><a href="moltk.Biosequence-class.html#__repr__" class="summary-sig-name">__repr__</a>(<span class="summary-sig-arg">...</span>)</span><br />
      __repr__( (Biosequence)arg1) -&gt; str :
    string representation</td>
          <td align="right" valign="top">
            
            
          </td>
        </tr>
      </table>
      
    </td>
  </tr>
<tr>
    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
      <table width="100%" cellpadding="0" cellspacing="0" border="0">
        <tr>
          <td><span class="summary-sig"><a href="moltk.Biosequence-class.html#__str__" class="summary-sig-name">__str__</a>(<span class="summary-sig-arg">...</span>)</span><br />
      __str__( (Biosequence)arg1) -&gt; object :</td>
          <td align="right" valign="top">
            
            
          </td>
        </tr>
      </table>
      
    </td>
  </tr>
<tr>
    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
      <table width="100%" cellpadding="0" cellspacing="0" border="0">
        <tr>
          <td><span class="summary-sig"><a href="moltk.Biosequence-class.html#fasta" class="summary-sig-name">fasta</a>(<span class="summary-sig-arg">...</span>)</span><br />
      fasta( (Biosequence)arg1) -&gt; str :
     Create a string representing the sequence in fasta format.</td>
          <td align="right" valign="top">
            
            
          </td>
        </tr>
      </table>
      
    </td>
  </tr>
<tr>
    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
      <table width="100%" cellpadding="0" cellspacing="0" border="0">
        <tr>
          <td><span class="summary-sig"><a href="moltk.Biosequence-class.html#get_description" class="summary-sig-name">get_description</a>(<span class="summary-sig-arg">...</span>)</span><br />
      get_description( (Biosequence)arg1) -&gt; str :</td>
          <td align="right" valign="top">
            
            
          </td>
        </tr>
      </table>
      
    </td>
  </tr>
<tr>
    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
      <table width="100%" cellpadding="0" cellspacing="0" border="0">
        <tr>
          <td><span class="summary-sig"><a href="moltk.Biosequence-class.html#get_number_of_residues" class="summary-sig-name">get_number_of_residues</a>(<span class="summary-sig-arg">...</span>)</span><br />
      get_number_of_residues( (Biosequence)arg1) -&gt; int :</td>
          <td align="right" valign="top">
            
            
          </td>
        </tr>
      </table>
      
    </td>
  </tr>
<tr>
    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
      <table width="100%" cellpadding="0" cellspacing="0" border="0">
        <tr>
          <td><span class="summary-sig"><a href="moltk.Biosequence-class.html#get_residue" class="summary-sig-name">get_residue</a>(<span class="summary-sig-arg">...</span>)</span><br />
      get_residue( (Biosequence)arg1, (int)ix) -&gt; BiosequenceResidue :</td>
          <td align="right" valign="top">
            
            
          </td>
        </tr>
      </table>
      
    </td>
  </tr>
<tr>
    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
      <table width="100%" cellpadding="0" cellspacing="0" border="0">
        <tr>
          <td><span class="summary-sig"><a href="moltk.Biosequence-class.html#load_fasta" class="summary-sig-name">load_fasta</a>(<span class="summary-sig-arg">...</span>)</span><br />
      load_fasta( (Biosequence)arg1, (str)file_name) -&gt; Biosequence :</td>
          <td align="right" valign="top">
            
            
          </td>
        </tr>
      </table>
      
    </td>
  </tr>
<tr>
    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
      <table width="100%" cellpadding="0" cellspacing="0" border="0">
        <tr>
          <td><span class="summary-sig"><a href="moltk.Biosequence-class.html#load_stream" class="summary-sig-name">load_stream</a>(<span class="summary-sig-arg">...</span>)</span><br />
      load_stream( (Biosequence)arg1, (object)is) -&gt; None :</td>
          <td align="right" valign="top">
            
            
          </td>
        </tr>
      </table>
      
    </td>
  </tr>
<tr>
    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
      <table width="100%" cellpadding="0" cellspacing="0" border="0">
        <tr>
          <td><span class="summary-sig"><a href="moltk.Biosequence-class.html#repr" class="summary-sig-name">repr</a>(<span class="summary-sig-arg">...</span>)</span><br />
      repr( (Biosequence)arg1) -&gt; str :
     repr is a helper for the python __repr__ method.</td>
          <td align="right" valign="top">
            
            
          </td>
        </tr>
      </table>
      
    </td>
  </tr>
<tr>
    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
      <table width="100%" cellpadding="0" cellspacing="0" border="0">
        <tr>
          <td><span class="summary-sig"><a href="moltk.Biosequence-class.html#write_fasta" class="summary-sig-name">write_fasta</a>(<span class="summary-sig-arg">...</span>)</span><br />
      write_fasta( (Biosequence)arg1, (object)os) -&gt; None :
     Write sequence in fasta format to a C++ stream.</td>
          <td align="right" valign="top">
            
            
          </td>
        </tr>
      </table>
      
    </td>
  </tr>
<tr>
    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
      <table width="100%" cellpadding="0" cellspacing="0" border="0">
        <tr>
          <td><span class="summary-sig"><a href="moltk.Biosequence-class.html#write_sequence_string" class="summary-sig-name">write_sequence_string</a>(<span class="summary-sig-arg">...</span>)</span><br />
      write_sequence_string( (Biosequence)arg1, (object)os) -&gt; None :
     Write a sequence string to a C++ stream.</td>
          <td align="right" valign="top">
            
            
          </td>
        </tr>
      </table>
      
    </td>
  </tr>
<tr>
    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
      <table width="100%" cellpadding="0" cellspacing="0" border="0">
        <tr>
          <td><span class="summary-sig"><a href="moltk.Biosequence-class.html#write_to_stream" class="summary-sig-name">write_to_stream</a>(<span class="summary-sig-arg">...</span>)</span><br />
      write_to_stream( (Biosequence)arg1, (object)os) -&gt; None :</td>
          <td align="right" valign="top">
            
            
          </td>
        </tr>
      </table>
      
    </td>
  </tr>
  <tr>
    <td colspan="2" class="summary">
    <p class="indent-wrapped-lines"><b>Inherited from <code><a href="moltk.BaseBiosequence-class.html">BaseBiosequence</a></code></b>:
      <code><a href="moltk.BaseBiosequence-class.html#__reduce__">__reduce__</a></code>
      </p>
    <p class="indent-wrapped-lines"><b>Inherited from <code><i>unreachable</i>.instance</code></b>:
      <code>__new__</code>
      </p>
    <p class="indent-wrapped-lines"><b>Inherited from <code>object</code></b>:
      <code>__delattr__</code>,
      <code>__format__</code>,
      <code>__getattribute__</code>,
      <code>__hash__</code>,
      <code>__reduce_ex__</code>,
      <code>__setattr__</code>,
      <code>__sizeof__</code>,
      <code>__subclasshook__</code>
      </p>
    </td>
  </tr>
</table>
<!-- ==================== CLASS VARIABLES ==================== -->
<a name="section-ClassVariables"></a>
<table class="summary" border="1" cellpadding="3"
       cellspacing="0" width="100%" bgcolor="white">
<tr bgcolor="#70b0f0" class="table-header">
  <td colspan="2" class="table-header">
    <table border="0" cellpadding="0" cellspacing="0" width="100%">
      <tr valign="top">
        <td align="left"><span class="table-header">Class Variables</span></td>
        <td align="right" valign="top"
         ><span class="options">[<a href="#section-ClassVariables"
         class="privatelink" onclick="toggle_private();"
         >hide private</a>]</span></td>
      </tr>
    </table>
  </td>
</tr>
<tr>
    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
        <a name="__instance_size__"></a><span class="summary-name">__instance_size__</span> = <code title="68">68</code>
    </td>
  </tr>
</table>
<!-- ==================== PROPERTIES ==================== -->
<a name="section-Properties"></a>
<table class="summary" border="1" cellpadding="3"
       cellspacing="0" width="100%" bgcolor="white">
<tr bgcolor="#70b0f0" class="table-header">
  <td colspan="2" class="table-header">
    <table border="0" cellpadding="0" cellspacing="0" width="100%">
      <tr valign="top">
        <td align="left"><span class="table-header">Properties</span></td>
        <td align="right" valign="top"
         ><span class="options">[<a href="#section-Properties"
         class="privatelink" onclick="toggle_private();"
         >hide private</a>]</span></td>
      </tr>
    </table>
  </td>
</tr>
  <tr>
    <td colspan="2" class="summary">
    <p class="indent-wrapped-lines"><b>Inherited from <code>object</code></b>:
      <code>__class__</code>
      </p>
    </td>
  </tr>
</table>
<!-- ==================== METHOD DETAILS ==================== -->
<a name="section-MethodDetails"></a>
<table class="details" border="1" cellpadding="3"
       cellspacing="0" width="100%" bgcolor="white">
<tr bgcolor="#70b0f0" class="table-header">
  <td colspan="2" class="table-header">
    <table border="0" cellpadding="0" cellspacing="0" width="100%">
      <tr valign="top">
        <td align="left"><span class="table-header">Method Details</span></td>
        <td align="right" valign="top"
         ><span class="options">[<a href="#section-MethodDetails"
         class="privatelink" onclick="toggle_private();"
         >hide private</a>]</span></td>
      </tr>
    </table>
  </td>
</tr>
</table>
<a name="__init__"></a>
<div>
<table class="details" border="1" cellpadding="3"
       cellspacing="0" width="100%" bgcolor="white">
<tr><td>
  <table width="100%" cellpadding="0" cellspacing="0" border="0">
  <tr valign="top"><td>
  <h3 class="epydoc"><span class="sig"><span class="sig-name">__init__</span>(<span class="sig-arg">...</span>)</span>
    <br /><em class="fname">(Constructor)</em>
  </h3>
  </td><td align="right" valign="top"
    >&nbsp;
    </td>
  </tr></table>
  
  <pre class="literalblock">

__init__( (object)arg1) -&gt; None :

    C++ signature :
        void __init__(struct _object *)

__init__( (object)arg1, (str)sequence [, (str)description='']) -&gt; None :

    C++ signature :
        void __init__(struct _object *,class std::basic_string&lt;char,struct std::char_traits&lt;char&gt;,class std::allocator&lt;char&gt; &gt; [,class std::basic_string&lt;char,struct std::char_traits&lt;char&gt;,class std::allocator&lt;char&gt; &gt;=''])

__init__( (object)arg1, (str)sequence [, (str)description='']) -&gt; None :

    C++ signature :
        void __init__(struct _object *,char const * [,class std::basic_string&lt;char,struct std::char_traits&lt;char&gt;,class std::allocator&lt;char&gt; &gt;=''])

__init__( (object)arg1, (Biosequence)rhs) -&gt; None :

    C++ signature :
        void __init__(struct _object *,class moltk::Biosequence)

</pre>
  <dl class="fields">
    <dt>Overrides:
        object.__init__
    </dt>
  </dl>
</td></tr></table>
</div>
<a name="__repr__"></a>
<div>
<table class="details" border="1" cellpadding="3"
       cellspacing="0" width="100%" bgcolor="white">
<tr><td>
  <table width="100%" cellpadding="0" cellspacing="0" border="0">
  <tr valign="top"><td>
  <h3 class="epydoc"><span class="sig"><span class="sig-name">__repr__</span>(<span class="sig-arg">...</span>)</span>
    <br /><em class="fname">(Representation operator)</em>
  </h3>
  </td><td align="right" valign="top"
    >&nbsp;
    </td>
  </tr></table>
  
  <pre class="literalblock">

__repr__( (Biosequence)arg1) -&gt; str :
    string representation

    C++ signature :
        class std::basic_string&lt;char,struct std::char_traits&lt;char&gt;,class std::allocator&lt;char&gt; &gt; __repr__(class moltk::Biosequence {lvalue})

</pre>
  <dl class="fields">
    <dt>Overrides:
        object.__repr__
    </dt>
  </dl>
</td></tr></table>
</div>
<a name="__str__"></a>
<div>
<table class="details" border="1" cellpadding="3"
       cellspacing="0" width="100%" bgcolor="white">
<tr><td>
  <table width="100%" cellpadding="0" cellspacing="0" border="0">
  <tr valign="top"><td>
  <h3 class="epydoc"><span class="sig"><span class="sig-name">__str__</span>(<span class="sig-arg">...</span>)</span>
    <br /><em class="fname">(Informal representation operator)</em>
  </h3>
  </td><td align="right" valign="top"
    >&nbsp;
    </td>
  </tr></table>
  
  <pre class="literalblock">

__str__( (Biosequence)arg1) -&gt; object :

    C++ signature :
        struct _object * __str__(class moltk::Biosequence {lvalue})

</pre>
  <dl class="fields">
    <dt>Overrides:
        object.__str__
    </dt>
  </dl>
</td></tr></table>
</div>
<a name="fasta"></a>
<div>
<table class="details" border="1" cellpadding="3"
       cellspacing="0" width="100%" bgcolor="white">
<tr><td>
  <table width="100%" cellpadding="0" cellspacing="0" border="0">
  <tr valign="top"><td>
  <h3 class="epydoc"><span class="sig"><span class="sig-name">fasta</span>(<span class="sig-arg">...</span>)</span>
  </h3>
  </td><td align="right" valign="top"
    >&nbsp;
    </td>
  </tr></table>
  
  <pre class="literalblock">

fasta( (Biosequence)arg1) -&gt; str :
     Create a string representing the sequence in fasta format.

    C++ signature :
        class std::basic_string&lt;char,struct std::char_traits&lt;char&gt;,class std::allocator&lt;char&gt; &gt; fasta(class moltk::Biosequence {lvalue})

</pre>
  <dl class="fields">
  </dl>
</td></tr></table>
</div>
<a name="get_description"></a>
<div>
<table class="details" border="1" cellpadding="3"
       cellspacing="0" width="100%" bgcolor="white">
<tr><td>
  <table width="100%" cellpadding="0" cellspacing="0" border="0">
  <tr valign="top"><td>
  <h3 class="epydoc"><span class="sig"><span class="sig-name">get_description</span>(<span class="sig-arg">...</span>)</span>
  </h3>
  </td><td align="right" valign="top"
    >&nbsp;
    </td>
  </tr></table>
  
  <pre class="literalblock">

get_description( (Biosequence)arg1) -&gt; str :

    C++ signature :
        class std::basic_string&lt;char,struct std::char_traits&lt;char&gt;,class std::allocator&lt;char&gt; &gt; get_description(class moltk::Biosequence {lvalue})

</pre>
  <dl class="fields">
  </dl>
</td></tr></table>
</div>
<a name="get_number_of_residues"></a>
<div>
<table class="details" border="1" cellpadding="3"
       cellspacing="0" width="100%" bgcolor="white">
<tr><td>
  <table width="100%" cellpadding="0" cellspacing="0" border="0">
  <tr valign="top"><td>
  <h3 class="epydoc"><span class="sig"><span class="sig-name">get_number_of_residues</span>(<span class="sig-arg">...</span>)</span>
  </h3>
  </td><td align="right" valign="top"
    >&nbsp;
    </td>
  </tr></table>
  
  <pre class="literalblock">

get_number_of_residues( (Biosequence)arg1) -&gt; int :

    C++ signature :
        unsigned int get_number_of_residues(class moltk::Biosequence {lvalue})

get_number_of_residues( (Biosequence)arg1) -&gt; int :

    C++ signature :
        unsigned int get_number_of_residues(struct Biosequence_wrapper {lvalue})

</pre>
  <dl class="fields">
    <dt>Overrides:
        <a href="moltk.BaseBiosequence-class.html#get_number_of_residues">BaseBiosequence.get_number_of_residues</a>
    </dt>
  </dl>
</td></tr></table>
</div>
<a name="get_residue"></a>
<div>
<table class="details" border="1" cellpadding="3"
       cellspacing="0" width="100%" bgcolor="white">
<tr><td>
  <table width="100%" cellpadding="0" cellspacing="0" border="0">
  <tr valign="top"><td>
  <h3 class="epydoc"><span class="sig"><span class="sig-name">get_residue</span>(<span class="sig-arg">...</span>)</span>
  </h3>
  </td><td align="right" valign="top"
    >&nbsp;
    </td>
  </tr></table>
  
  <pre class="literalblock">

get_residue( (Biosequence)arg1, (int)ix) -&gt; BiosequenceResidue :

    C++ signature :
        class moltk::BiosequenceResidue get_residue(class moltk::Biosequence {lvalue},unsigned int)

</pre>
  <dl class="fields">
    <dt>Overrides:
        <a href="moltk.BaseBiosequence-class.html#get_residue">BaseBiosequence.get_residue</a>
    </dt>
  </dl>
</td></tr></table>
</div>
<a name="load_fasta"></a>
<div>
<table class="details" border="1" cellpadding="3"
       cellspacing="0" width="100%" bgcolor="white">
<tr><td>
  <table width="100%" cellpadding="0" cellspacing="0" border="0">
  <tr valign="top"><td>
  <h3 class="epydoc"><span class="sig"><span class="sig-name">load_fasta</span>(<span class="sig-arg">...</span>)</span>
  </h3>
  </td><td align="right" valign="top"
    >&nbsp;
    </td>
  </tr></table>
  
  <pre class="literalblock">

load_fasta( (Biosequence)arg1, (str)file_name) -&gt; Biosequence :

    C++ signature :
        class moltk::Biosequence {lvalue} load_fasta(class moltk::Biosequence {lvalue},class std::basic_string&lt;char,struct std::char_traits&lt;char&gt;,class std::allocator&lt;char&gt; &gt;)

load_fasta( (Biosequence)arg1, (object)is) -&gt; Biosequence :

    C++ signature :
        class moltk::Biosequence {lvalue} load_fasta(class moltk::Biosequence {lvalue},class std::basic_istream&lt;char,struct std::char_traits&lt;char&gt; &gt; {lvalue})

</pre>
  <dl class="fields">
  </dl>
</td></tr></table>
</div>
<a name="load_stream"></a>
<div>
<table class="details" border="1" cellpadding="3"
       cellspacing="0" width="100%" bgcolor="white">
<tr><td>
  <table width="100%" cellpadding="0" cellspacing="0" border="0">
  <tr valign="top"><td>
  <h3 class="epydoc"><span class="sig"><span class="sig-name">load_stream</span>(<span class="sig-arg">...</span>)</span>
  </h3>
  </td><td align="right" valign="top"
    >&nbsp;
    </td>
  </tr></table>
  
  <pre class="literalblock">

load_stream( (Biosequence)arg1, (object)is) -&gt; None :

    C++ signature :
        void load_stream(class moltk::Biosequence {lvalue},class std::basic_istream&lt;char,struct std::char_traits&lt;char&gt; &gt; {lvalue})

</pre>
  <dl class="fields">
  </dl>
</td></tr></table>
</div>
<a name="repr"></a>
<div>
<table class="details" border="1" cellpadding="3"
       cellspacing="0" width="100%" bgcolor="white">
<tr><td>
  <table width="100%" cellpadding="0" cellspacing="0" border="0">
  <tr valign="top"><td>
  <h3 class="epydoc"><span class="sig"><span class="sig-name">repr</span>(<span class="sig-arg">...</span>)</span>
  </h3>
  </td><td align="right" valign="top"
    >&nbsp;
    </td>
  </tr></table>
  
  <pre class="literalblock">

repr( (Biosequence)arg1) -&gt; str :
     repr is a helper for the python __repr__ method.

    C++ signature :
        class std::basic_string&lt;char,struct std::char_traits&lt;char&gt;,class std::allocator&lt;char&gt; &gt; repr(class moltk::Biosequence {lvalue})

</pre>
  <dl class="fields">
  </dl>
</td></tr></table>
</div>
<a name="write_fasta"></a>
<div>
<table class="details" border="1" cellpadding="3"
       cellspacing="0" width="100%" bgcolor="white">
<tr><td>
  <table width="100%" cellpadding="0" cellspacing="0" border="0">
  <tr valign="top"><td>
  <h3 class="epydoc"><span class="sig"><span class="sig-name">write_fasta</span>(<span class="sig-arg">...</span>)</span>
  </h3>
  </td><td align="right" valign="top"
    >&nbsp;
    </td>
  </tr></table>
  
  <pre class="literalblock">

write_fasta( (Biosequence)arg1, (object)os) -&gt; None :
     Write sequence in fasta format to a C++ stream.

    C++ signature :
        void write_fasta(class moltk::Biosequence {lvalue},class std::basic_ostream&lt;char,struct std::char_traits&lt;char&gt; &gt; {lvalue})

write_fasta( (Biosequence)arg1, (str)file_name) -&gt; None :
     Write sequence in fasta format to a designated file.

    C++ signature :
        void write_fasta(class moltk::Biosequence {lvalue},class std::basic_string&lt;char,struct std::char_traits&lt;char&gt;,class std::allocator&lt;char&gt; &gt;)

</pre>
  <dl class="fields">
  </dl>
</td></tr></table>
</div>
<a name="write_sequence_string"></a>
<div>
<table class="details" border="1" cellpadding="3"
       cellspacing="0" width="100%" bgcolor="white">
<tr><td>
  <table width="100%" cellpadding="0" cellspacing="0" border="0">
  <tr valign="top"><td>
  <h3 class="epydoc"><span class="sig"><span class="sig-name">write_sequence_string</span>(<span class="sig-arg">...</span>)</span>
  </h3>
  </td><td align="right" valign="top"
    >&nbsp;
    </td>
  </tr></table>
  
  <pre class="literalblock">

write_sequence_string( (Biosequence)arg1, (object)os) -&gt; None :
     Write a sequence string to a C++ stream.  The sequence description is NOT included.

    C++ signature :
        void write_sequence_string(class moltk::Biosequence {lvalue},class std::basic_ostream&lt;char,struct std::char_traits&lt;char&gt; &gt; {lvalue})

</pre>
  <dl class="fields">
  </dl>
</td></tr></table>
</div>
<a name="write_to_stream"></a>
<div>
<table class="details" border="1" cellpadding="3"
       cellspacing="0" width="100%" bgcolor="white">
<tr><td>
  <table width="100%" cellpadding="0" cellspacing="0" border="0">
  <tr valign="top"><td>
  <h3 class="epydoc"><span class="sig"><span class="sig-name">write_to_stream</span>(<span class="sig-arg">...</span>)</span>
  </h3>
  </td><td align="right" valign="top"
    >&nbsp;
    </td>
  </tr></table>
  
  <pre class="literalblock">

write_to_stream( (Biosequence)arg1, (object)os) -&gt; None :

    C++ signature :
        void write_to_stream(class moltk::Biosequence {lvalue},class std::basic_ostream&lt;char,struct std::char_traits&lt;char&gt; &gt; {lvalue})

write_to_stream( (Biosequence)arg1, (object)os) -&gt; None :

    C++ signature :
        void write_to_stream(struct Biosequence_wrapper {lvalue},class std::basic_ostream&lt;char,struct std::char_traits&lt;char&gt; &gt; {lvalue})

</pre>
  <dl class="fields">
    <dt>Overrides:
        <a href="moltk.BaseBiosequence-class.html#write_to_stream">BaseBiosequence.write_to_stream</a>
    </dt>
  </dl>
</td></tr></table>
</div>
<br />
<!-- ==================== NAVIGATION BAR ==================== -->
<table class="navbar" border="0" width="100%" cellpadding="0"
       bgcolor="#a0c0ff" cellspacing="0">
  <tr valign="middle">
  <!-- Home link -->
      <th>&nbsp;&nbsp;&nbsp;<a
        href="moltk-module.html">Home</a>&nbsp;&nbsp;&nbsp;</th>

  <!-- Tree link -->
      <th>&nbsp;&nbsp;&nbsp;<a
        href="module-tree.html">Trees</a>&nbsp;&nbsp;&nbsp;</th>

  <!-- Index link -->
      <th>&nbsp;&nbsp;&nbsp;<a
        href="identifier-index.html">Indices</a>&nbsp;&nbsp;&nbsp;</th>

  <!-- Help link -->
      <th>&nbsp;&nbsp;&nbsp;<a
        href="help.html">Help</a>&nbsp;&nbsp;&nbsp;</th>

  <!-- Project homepage -->
      <th class="navbar" align="right" width="100%">
        <table border="0" cellpadding="0" cellspacing="0">
          <tr><th class="navbar" align="center"
            ><a class="navbar" target="_top" href="http://moltk.rotatingpenguin.com/">MolTK python API v0.4.0 Documentation</a></th>
          </tr></table></th>
  </tr>
</table>
<table border="0" cellpadding="0" cellspacing="0" width="100%%">
  <tr>
    <td align="left" class="footer">
    Generated by Epydoc 3.0.1 on Fri Nov 04 20:07:18 2011
    </td>
    <td align="right" class="footer">
      <a target="mainFrame" href="http://epydoc.sourceforge.net"
        >http://epydoc.sourceforge.net</a>
    </td>
  </tr>
</table>

<script type="text/javascript">
  <!--
  // Private objects are initially displayed (because if
  // javascript is turned off then we want them to be
  // visible); but by default, we want to hide them.  So hide
  // them unless we have a cookie that says to show them.
  checkCookie();
  // -->
</script>
</body>
</html>
